Figure S1 | Atomic models in cryo-EM maps. (a) Two alpha (blue) and two beta (green) subunits of the T20S proteasome are shown
as cartoon tubes fitted in a 3.2 Å potential map at isolevel 0.25 (EMDB 5623, PDB 3J9I). (b) The same subunits are depicted in
density at a higher isolevel of 0.35, where sharper features of side chain density can be observed. (c) Two subunits of the TrpV1
tetramer are shown in green and blue in a 3.27Å potential map at an isolevel of 10 (EMDB 5778, PDB 3J9J)
Figure S2 | EMRinger Score is unaffected by model size. (a) EMRinger plot for a 366 amino acid monomer of the Hepatitis B virus
capsid gives a peak EMRinger score of 3.25 (EMDB 2278, PDB 3J2V). (b) Histogram of EMRinger map value peaks above threshold
6.090 (the threshold of maximum EMRinger score) for the monomer in density. (c) EMRinger plot for the full biological 21960 amino
acid 60-mer assembly of the Hepatitis B capsid gives a nearly identical set of scores to the monomer, with a peak score of 3.16. The
smoother plot is likely due to the averaging out of artifacts due to grid sampling. (d) Histogram of EMRinger map value peaks above
threshold 5.726 (the threshold of maximum EMRinger score) for the 60-mer in density.
Figure S3| Histogram of peak counts for EMRinger scan of T20S Proteasome (EMDB 5778, PDB 3J9I) at a map value threshold of
0.242 e-/Å3. At this threshold, which maximizes the EMRinger score, 1547 rotameric peaks (blue) greatly outnumber 555 nonrotameric peaks (red).
Table S1 | EMRinger analysis of selected maps above 5 Å resolution with atomic models. For the transmembrane-only scan of the
TrpV1 Channel (EMDB 5778), residues 381-695 of each chain of the deposited model (PDB 3J5P) were used.
EMDB ID
PDB ID
Scannable
Resolution Model
EMRinger
(Å)
Length
Score
Description
5256
3IZX
3.1
2427
1.54
Cytoplasmic Polyhedrosis Virus1
2012
5995
3J7H
3.2
2616
2.04
Beta-Galactosidase2
2014
5160
3IYL
3.2
5708
2.18
Aquareovirus3
2010
5623
3J9I
3.2
3439
3.05
T20S Proteasome4
2013
5778
3J5P
3.27
1484
0.56
TrpV1 Channel5
2014
5778 (TM only)
3J5P
3.27
792
1.17
TrpV1 Channel5
2014
5778 (Refined)
3J9J
3.27
876
2.58
TrpV1 Channel
2015
2513
4CIO
3.36
521
1.29
F420 reducing hydrogenase6
2013
2787
4V19,
4V1A
1.85
Mammalian Mitochondrial Ribosome,
Large Subunit7
2014
2014
3.4
5326
Year
2762
3J7Y
3.4
4806
2.09
Human Mitochondrial Ribosome Large
Subunit8
6035
3J7W
3.5
1267
0.96
Bacteriophage T7 capsid9
2014
5764
3J4U
3.5
1757
1.95
Bordetella bacteriophage10
2014
2278
3J2V
3.5
366
3.26
Hepatitis B Virus Core11
2013
5925
3J6J
3.6
528
1.23
MAVS filament11
2014
2764
3J80
3.75
3060
0.9
40S-eIF1-eIF1A preinitiation complex12
2014
2773
4UY8
3.8
1976
0.36
TnaC stalled E.coli ribosome13
2014
5830
3J63
3.8
915
1.05
ASC Pyrin Domain14
2014
6000
3J7L
3.8
259
2.08
Brome Mosaic Virus15
2014
2763
3J81
4
3225
0.54
Partial Yeast 48S preinitiation complex12 2014
5600
3J3I
4.1
604
0.18
Penicillium Chrysogenum Virus16
2014
2364
4BTG
4.4
898
-0.47
Bacteriophage phi procapsid17
2013
2677
4UPC
4.5
235
-0.41
Human Gamma-secretase18
2014
2273
3ZIF
4.5
7430
0.13
Bovine Adenovirus 319
2014
5678
3J40
4.5
1848
0.49
Bacteriophage epsilon1520
2013
5645
3J3X
4.6
4528
-0.05
Mm Chaperonin, Training21
2013
5895
3J6E
4.7
4705
0.09
GMPCPP Microtubule22
2014
5646
3J3X
4.7
4528
0.55
Mm Chaperonin, Testing21
2013
2788
4V1W
4.7
2976
1.27
Horse spleen apoferritin23
2014
5391
3J1B
4.9
4816
0.2
apo rATcpn-alpha24
2013
6187
3J8X
5
737
-0.71
Empty Microtubule/Kinesin25
2014
6188
3J8Y
5
744
-0.16
ADP-AlF3 Microtubule/Kinesin25
2014
5896
3J6F
5
4706
0.06
GDP microtubule22
2014
5886
3J69
5
579
0.8
nanobody/poliovirus26
2014
Figure S4| Adjusted EMRinger Score degrades rapidly with decreasing resolution. The T20S proteasome map (EMDB 5623, PDB
1PMA) is low-pass filtered to resolutions ranging from 3.2 to 7 Å. EMRinger scores for each of these filtered maps show a resolution
dependence and that by 5 Å resolution side chains are no longer distinguishable from noise and the EMRinger score is near 0.
Figure S5 | Histograms of TrpV1 models at multiple map value thresholds. (a) Histograms at thresholds of 4, 8, 12, and 16 for
EMRinger map value peaks of the transmembrane region of the deposited TrpV1 model (EMDB 5778, PDB 3J5P). (b) Histograms at
thresholds of 4, 8, 12, and 16 for the EMRinger map value peaks of the transmembrane region of TrpV1 refined by RosettaCM show
improved enrichment at rotameric positions at all thresholds.
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